base_count.sh

#! /usr/bin/bash

op_perl0() {
    perl -lnE '
        BEGIN{ say "filename A G C T N" }
        unless (($. + 2) % 4) {
            $i = 0;
            ++$b{$c} while ($c=substr($_, $i++, 1));
            # s/(.)/++$b{$1}/ge;

            # for ($i = 0; $i < length; $i++) {
            #     ++$b{substr($_, $i, 1)}
            # }
        }
        $,=" ", say($c, @b{A,G,C,T,N}), $c=$ARGV, undef %b if (eof() || (($c//=$ARGV) ne $ARGV))
    ' *.fastq | column -t -o ' | '
}

op_perl1() {
    perl -lnE '
        BEGIN{ say "filename A G C T N" }
        map {++$b{$_}} split// unless ($.+2)%4;
        $,=" ", say($c, @b{A,G,C,T,N}), $c=$ARGV, undef %b if (eof() || (($c//=$ARGV) ne $ARGV))
    ' *.fastq | column -t -o ' | '
}

op_perl2() {
    perl -lE '
        BEGIN {say "filename A G C T N"}
        while ($f = shift) {
            %b = ();
            open(F, $f) and @d = <F>;
            for ($i = 1; $i <= $#d; $i += 4) {
                map {++$b{$_}} split //, $d[$i];
            }
            $,=" ", say $f, @b{A, G, C, T, N};
        }
    ' *.fastq | column -t -o ' | '
}

op_python() {
    python -c 'print("filename A G C T N") or [
        (c := __import__("collections").Counter())
        or [[
            c.update(d.strip())
            for i, d in enumerate(open(f).readlines()) if i % 4 == 1
        ],
            print(f, " ".join(str(c[k]) for k in "AGCTN"))]
        for f in __import__("sys").argv[1:]
    ]
    ' *.fastq | column -t -o ' | '
}

op_pipeline() {
    {
        echo filename A G C T N
        for f in *.fastq; do
            sed -n '2~4p' $f | grep -o . | sort | uniq -c | \
                sort -k2 | awk 'BEGIN{printf "'$f' "} {print $1}' | tr '\n' ' '
            echo
        done
    } | awk '{print $1, $2, $4, $3, $6, $5}' | column -t -o ' | '
}

op_awk() {
    awk '
        BEGIN{
            print "filename A G C G N"
            for (fn = 1; fn < ARGC; fn++) {
                ln = 0
                while ((getline line < ARGV[fn]) > 0) {
                    if (++ln % 4 == 2) {
                        len = length(line)
                        for (i = 1; i <= len; i++)
                            ++count[substr(line, i, 1)];
                    }
                }
                print ARGV[fn], count["A"], count["G"], count["C"], count["T"], count["N"]
                close(ARGV[fn])
                delete count
            }
        }
    ' *.fastq | column -t -o ' | '
}

op_bash() {
    {
        echo filename A C G N T
        for f in *.fastq; do
            declare -A alphaCount
            lineNumber=0

            while IFS= read -r line; do
                if [[ $(($((lineNumber++)) % 4)) = 1 ]]; then
                    for (( i=0; i<${#line}; i++ )); do
                        alphaCount["${line:$i:1}"]=$((${alphaCount["${line:$i:1}"]:-0}+1))
                    done
                fi
            done < $f

            echo "$f ${alphaCount[A]} ${alphaCount[G]} ${alphaCount[C]} ${alphaCount[T]} ${alphaCount[N]}"

            unset alphaCount
        done
    } | column -t -o ' | '
}

op_tcl() {
    {
        tclsh /dev/stdin *.fastq <<'EOF'
        puts "filename A G C T N"

        foreach filename $argv {
            set fh [open $filename]
            set line_number 0
            set counter [dict create]

            while {[gets $fh line] >= 0} {
                if {[expr $line_number % 4 == 1]} {
                    foreach letter [split $line ""] {
                        dict incr counter $letter
                    }
                }
                incr line_number
            }
            # close $fh

            puts -nonewline "$filename"

            foreach letter [split AGCTN ""] {
                puts -nonewline " [dict get $counter $letter]"
            }

            puts ""
        }
EOF
    } | column -t -o ' | '
}

timeit() {
    start_time="$(date -u +%s.%N)"
    $@
    end_time="$(date -u +%s.%N)"
    elapsed="$(bc <<<"$end_time-$start_time")"
    printf "eplapsed time: %.3fs\n" $elapsed
}

echo 'perl0:' && timeit op_perl1 && echo
echo 'perl1:' && timeit op_perl1 && echo
echo 'perl2:' && timeit op_perl2 && echo
echo 'python:' && timeit op_python && echo
echo 'awk:' && timeit op_awk && echo
echo 'tcl:' && timeit op_tcl && echo
echo 'pipeline:' && timeit op_pipeline && echo
echo 'bash:' && timeit op_bash

# python:   1.553s
# perl2:    3.242s
# perl0:    3.335s
# perl1:    3.354s
# awk:      4.512s
# tcl:      17.465s
# pipeline: 19.209s
# bash:     667.201s